hic
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Published
20 hours ago •
nf-core
nf-core
java error
Description of the bug
I am consistently getting a ominous java error with -profile singularity. I tried with different java versions
openjdk 11.0.1 2018-10-16 LTS
openjdk 17.0.8-internal 2023-07-18
openjdk 20.0.1 2023-04-18
but it doesnt seem to make a difference. The command and output are described below. I also tried -profile charliecloud, but here a different java error comes up:
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (1)'
Caused by:
java.nio.channels.OverlappingFileLockException
with -profile conda the workflow at least starts, so I know my sample sheet and the other parameters are functional. But then it quickly fails with
[[id:Sample_1, single_end:false, chunk:0], [/lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119399_Track-163672_R1.fastq.gz, /lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119399_Track-163672_R2.fastq.gz]]
[[id:Sample_2, single_end:false, chunk:0], [/lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119400_Track-163673_R1.fastq.gz, /lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119400_Track-163673_R2.fastq.gz]]
[[id:Sample_3, single_end:false, chunk:0], [/lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119401_Track-163720_R1.fastq.gz, /lustre/projects/dazzlerAssembly/asm_mGlyDav/data/hic/L119401_Track-163720_R2.fastq.gz]]
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})'
Caused by:
Process `NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})` terminated with an error exit status (1)
Command executed:
cooler makebins \
\
asm_mGlyDav.hap1.deepVariant.fasta.sizes \
40000 > cooler_bins_40000.bed
cat <<-END_VERSIONS > versions.yml
"NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS":
cooler: $(cooler --version 2>&1 | sed 's/cooler, version //')
END_VERSIONS
Command exit status:
1
Command output:
(empty)
Command error:
Traceback (most recent call last):
File "/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/bin/cooler", line 6, in <module>
from cooler.cli import cli
File "/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.10/site-packages/cooler/__init__.py", line 14, in <module>
from .api import Cooler, annotate
File "/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.10/site-packages/cooler/api.py", line 13, in <module>
from .core import (
File "/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.10/site-packages/cooler/core.py", line 3, in <module>
from pandas.api.types import is_categorical
ImportError: cannot import name 'is_categorical' from 'pandas.api.types' (/tmp/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.10/site-packages/pandas/api/types/__init__.py)
Work dir:
/tmp/24/4c78bfcda8b18319e8e1e21bd213bc
So three different error messages... I would really like to get -profile singularity to work, but have no idea on how to proceed. Could you point me in the right direction, please?
Thank you very much.
Command used and terminal output
nextflow run nf-core/hic --input /lustre/projects/dazzlerAssembly/test_nf_hic/samplesheet.csv --outdir /lustre/projects/dazzlerAssembly/test_nf_hic/hic_results -profile singularity -w /tmp/ --fasta /lustre/projects/dazzlerAssembly/asm_mGlyDav/assembly/polishing/hap1/asm_mGlyDav.hap1.deepVariant.fasta --restriction_site '^GATC,G^ANTC,C^TNAG,T^TAA' --ligation_site 'GATCGATC,GATCANTC,GANTGATC,GANTANTC,GATCTNAG,GANTTNAG,CTNAGATC,CTNAANTC,TTAGATC,TTAANTC,TTATTNAG,GATCTAA,GANTTAA,CTNATAA,TTATAA,CTNATNAG'
N E X T F L O W ~ version 23.04.2
Launching `https://github.com/nf-core/hic` [tiny_noether] DSL2 - revision: fe4ac65631 [master]
------------------------------------------------------
,--./,-.
___ __ __ __ ___ /,-._.--~'
|\ | |__ __ / ` / \ |__) |__ } {
| \| | \__, \__/ | \ |___ \`-._,-`-,
`._,._,'
nf-core/hic v2.1.0-gfe4ac65
------------------------------------------------------
Core Nextflow options
revision : master
runName : tiny_noether
containerEngine : singularity
launchDir : /tmp
workDir : /tmp
projectDir : /home/uelze/.nextflow/assets/nf-core/hic
userName : uelze
profile : singularity
configFiles : /home/uelze/.nextflow/assets/nf-core/hic/nextflow.config
Input/output options
input : /lustre/projects/dazzlerAssembly/test_nf_hic/samplesheet.csv
outdir : /lustre/projects/dazzlerAssembly/test_nf_hic/hic_results
Reference genome options
fasta : /lustre/projects/dazzlerAssembly/asm_mGlyDav/assembly/polishing/hap1/asm_mGlyDav.hap1.deepVariant.fasta
Digestion Hi-C
restriction_site : ^GATC,G^ANTC,C^TNAG,T^TAA
ligation_site : GATCGATC,GATCANTC,GANTGATC,GANTANTC,GATCTNAG,GANTTNAG,CTNAGATC,CTNAANTC,TTAGATC,TTAANTC,TTATTNAG,GATCTAA,GANTTAA,CTNATAA,TTATAA,CTNATNAG
DNAse Hi-C
min_cis_dist : 0
Alignments
bwt2_opts_end2end : --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder
bwt2_opts_trimmed : --very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder
Valid Pairs Detection
max_insert_size : 0
min_insert_size : 0
max_restriction_fragment_size: 0
min_restriction_fragment_size: 0
Contact maps
bin_size : 1000000
ice_filter_high_count_perc : 0
res_zoomify : null
Downstream Analysis
res_dist_decay : 250000
tads_caller : insulation
res_tads : 40000
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/hic for your analysis please cite:
* The pipeline
https://doi.org/10.5281/zenodo.2669513
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/hic/blob/master/CITATIONS.md
------------------------------------------------------
[- ] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK -
[- ] process > NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK -
[- ] process > NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD -
[- ] process > NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES -
[- ] process > NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS -
[- ] process > NFCORE_HIC:HIC:FASTQC -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2 -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES -
[- ] process > NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION -
[- ] process > NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION -
[- ] process > NFCORE_HIC:HIC:HICPRO:MERGE_STATS -
[- ] process > NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS -
[- ] process > NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS -
[- ] process > NFCORE_HIC:HIC:COOLER:COOLER_CLOAD -
[- ] process > NFCORE_HIC:HIC:COOLER:COOLER_BALANCE -
[- ] process > NFCORE_HIC:HIC:COOLER:COOLER_ZOOMIFY -
[- ] process > NFCORE_HIC:HIC:COOLER:COOLER_DUMP -
[- ] process > NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP -
[- ] process > NFCORE_HIC:HIC:HIC_PLOT_DIST_VS_COUNTS -
[- ] process > NFCORE_HIC:HIC:COMPARTMENTS:COOLTOOLS_EIGSCIS -
[- ] process > NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION -
[- ] process > NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS -
[- ] process > NFCORE_HIC:HIC:MULTIQC -
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK'
Caused by:
java.io.IOException: Function not implemented
-- Check '.nextflow.log' file for details
Relevant files
No response
System information
No response
Hi,
I'm afraid the error is not related to the nf-core-hic pipeline itself, but more to the env or the config. Did you try to ask for help in the slack forum ?
